Changeset 24639

Timestamp:

03/04/20 20:42:07 (5 years ago)

Author:

jdquinn

Message:

CHG: Changing to PETSc 3.11 as this works with Dakota 6.2; cleanup

Location:

issm/trunk-jpl

Files:

• externalpackages/dakota/install-6.2-linux-static.sh (modified) (3 diffs)
• externalpackages/dakota/install-6.2-linux.sh (modified) (4 diffs)
• externalpackages/dakota/install-6.2-linux64-petsclibs.sh (deleted)
• externalpackages/dakota/install-6.2-linux64-static.sh (deleted)
• externalpackages/dakota/install-6.2-linux64.sh (deleted)
• externalpackages/petsc/install-3.11-linux-static.sh (copied) (copied from issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-static.sh ) (1 diff)
• externalpackages/petsc/install-3.11-mac-static.sh (copied) (copied from issm/trunk-jpl/externalpackages/petsc/install-3.12-linux-static.sh ) (1 diff)
• externalpackages/petsc/install-3.11-mac.sh (modified) (1 diff)
• jenkins/jenkins.sh (modified) (11 diffs)
• jenkins/macosx_pine-island (modified) (1 diff)
• jenkins/ross-debian_linux (modified) (1 diff)
• jenkins/ross-debian_linux-adolc-ampioff (modified) (1 diff)
• jenkins/ross-debian_linux-adolc-ampion (modified) (1 diff)
• jenkins/ross-debian_linux-binaries (modified) (1 diff)
• jenkins/ross-debian_linux-binaries-with_dakota (modified) (1 diff)
• jenkins/ross-debian_linux-codipack (modified) (1 diff)
• jenkins/ross-debian_linux-dakota (modified) (1 diff)
• jenkins/ross-debian_linux-gia (modified) (1 diff)
• jenkins/ross-debian_linux-iceocean (modified) (1 diff)
• jenkins/ross-debian_linux-python (modified) (1 diff)
• jenkins/ross-debian_linux-solid_earth (modified) (1 diff)

issm/trunk-jpl/externalpackages/dakota/install-6.2-linux-static.sh

@@ -6 +6 @@
 #
 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
-MPI_INSTALL=${ISSM_DIR}/externalpackages/petsc/install
 VER="6.2"
 
 ## Environment
 #
-export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lf2cblas -L/usr/lib/gcc/x86_64-linux-gnu/8 -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
+export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L${ISSM_DIR}/lib -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
 export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version)
@@ -18 +17 @@
 export DAK_INSTALL=${DAK_ROOT}/install
 export DAK_SRC=${DAK_ROOT}/src
-export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lf2clapack -L/usr/lib/gcc/x86_64-linux-gnu/8 -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
-export MPIHOME=${MPI_INSTALL} # This appears to only be used by certain external packages and examples
+export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L${ISSM_DIR}/lib -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
 
 # Cleanup
@@ -49 +47 @@
         -DBUILD_SHARED_LIBS=OFF \
         -DBUILD_STATIC_LIBS=ON \
-        -DCMAKE_C_COMPILER=${MPI_INSTALL}/bin/mpicc \
-        -DCMAKE_CXX_COMPILER=${MPI_INSTALL}/bin/mpicxx \
-        -DCMAKE_Fortran_COMPILER=${MPI_INSTALL}/bin/mpif77 \
+        -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \
+        -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
+        -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
         -DCMAKE_C_FLAGS="-fPIC" \
         -DCMAKE_CXX_FLAGS="-fPIC" \

issm/trunk-jpl/externalpackages/dakota/install-6.2-linux.sh

@@ -6 +6 @@
 #
 DAK_ROOT=${ISSM_DIR}/externalpackages/dakota
-MPI_INSTALL=${ISSM_DIR}/externalpackages/petsc/install
 VER="6.2"
 
 ## Environment
 #
-export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lf2cblas" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
+export BLAS_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lfblas -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export BLAS_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
 export BOOST_ROOT=${ISSM_DIR}/externalpackages/boost/install
 export CXXFLAGS='-std=c++98' # Setting CXXFLAGS to deal with C++11 incompatibility with Matlab's Boost (absolutely necessary for this version)
@@ -18 +17 @@
 export DAK_INSTALL=${DAK_ROOT}/install
 export DAK_SRC=${DAK_ROOT}/src
-export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lf2clapack" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
-export MPIHOME=${MPI_INSTALL} # This appears to only be used by certain external packages and examples
+export LAPACK_LIBS="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lflapack -L/usr/lib/x86_64-linux-gnu -lgfortran" # Need to export LAPACK_LIBS *and* pass it as an option to CMake to ensure that external packages also find it
 
 # Cleanup
@@ -25 +23 @@
 mkdir build install src
 
-#Download from ISSM server
+# Download source
 ${ISSM_DIR}/scripts/DownloadExternalPackage.sh "https://issm.ess.uci.edu/files/externalpackages/dakota-${VER}-public.src.tar.gz" "dakota-${VER}-public-src.tar.gz"
 
@@ -49 +47 @@
         -DBUILD_SHARED_LIBS=ON \
         -DBUILD_STATIC_LIBS=OFF \
-        -DCMAKE_C_COMPILER=${MPI_INSTALL}/bin/mpicc \
-        -DCMAKE_CXX_COMPILER=${MPI_INSTALL}/bin/mpicxx \
-        -DCMAKE_Fortran_COMPILER=${MPI_INSTALL}/bin/mpif77 \
+        -DCMAKE_C_COMPILER=${MPI_HOME}/bin/mpicc \
+        -DCMAKE_CXX_COMPILER=${MPI_HOME}/bin/mpicxx \
+        -DCMAKE_Fortran_COMPILER=${MPI_HOME}/bin/mpif77 \
         -DHAVE_ACRO=OFF \
         -DHAVE_JEGA=OFF \

issm/trunk-jpl/externalpackages/petsc/install-3.11-linux-static.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="3.12.3"
+VER="3.11.3"
 
 # Download source

issm/trunk-jpl/externalpackages/petsc/install-3.11-mac-static.sh

@@ -5 +5 @@
 ## Constants
 #
-VER="3.12.3"
+VER="3.11.3"
 
 # Download source

issm/trunk-jpl/externalpackages/petsc/install-3.11-mac.sh

@@ -26 +26 @@
         --prefix="${ISSM_DIR}/externalpackages/petsc/install" \
         --PETSC_DIR="${ISSM_DIR}/externalpackages/petsc/src" \
+        --COPTFLAGS="-O2" \
+        --CXXOPTFLAGS="-O2" \
+        --FOPTFLAGS="-O2" \
         --with-debugging=0 \
         --with-valgrind=0 \

issm/trunk-jpl/jenkins/jenkins.sh

@@ -16 +16 @@
 rm -rf $ISSM_DIR/execution/*
 rm -rf $ISSM_DIR/nightlylog
-mkdir  $ISSM_DIR/nightlylog
+mkdir $ISSM_DIR/nightlylog
 
 #Server URI
@@ -31 +31 @@
 if [ ! -f "$1" ]
 then
-        echo "File $1 not found!" >&2   # Error message to stderr.
+        echo "File $1 not found!" >&2 # Error message to stderr.
         exit 1
 fi
@@ -67 +67 @@
         SVN_CURRENT=$SVN_REVISION_1
         echo "Previous revision number: $SVN_PREVIOUS"
-        echo "Current  revision number: $SVN_CURRENT"
+        echo "Current revision number: $SVN_CURRENT"
 
         # Get list of changed files
@@ -82 +82 @@
         #cat changes | grep 'document_edit' |sed -e 's/document_edit.png/document_edit.png\
                 #/g' | sed -e 's/.*<\/a><\/td><td>\(.*\)<\/td><\/tr>.*/\1/' | grep -v 'document_edit.png' > $ISSM_DIR/TEMP
-        cat changes  | tr " " "\n" | grep trunk | sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
+        cat changes | tr " " "\n" | grep trunk | sed -e 's/.*<a>\(.*\)<\/a>.*/\1/' > $ISSM_DIR/TEMP
 
         # Print list of changed files
@@ -146 +146 @@
 echo $SVN_REVISION_1 > $ISSM_DIR/svn_revision_old
 #}}}
-#Install external packages    (ISSM_EXTERNALPACKAGES){{{
-
-#number of packages:
-NUMPACKAGES=$(($(echo $EXTERNALPACKAGES | wc -w )/2))
+
+## External Packages
+#
+
+# Number of packages
+NUMPACKAGES=$(($(echo ${EXTERNALPACKAGES} | wc -w ) / 2))
 
 #Jenkins xml files for individual packages
@@ -315 +317 @@
         warning off %necessary to avoid a log of several Go for parallel runs
         try,
-        $(if [ "$MATLAB_NROPTIONS" = ""  ]
-        then
+        $(if [ "$MATLAB_NROPTIONS" = "" ]; then
                 echo "runme('output','nightly','rank',$i,'numprocs',$NUMCPUS_RUN);"
         else
@@ -374 +375 @@
 for job in `jobs -p`
 do
-echo "Waiting on: $job"
-    wait $job
+        echo "Waiting on: $job"
+        wait $job
 done
 
@@ -411 +412 @@
         for job in `jobs -p`
         do
-        echo "Waiting on: $job"
-            wait $job
+                echo "Waiting on: $job"
+                wait $job
         done
 
@@ -535 +536 @@
 if [ $MATLAB_TEST -eq 1 ]; then
         #number tests:
-        numtests=`cat matlab_log.log  | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
-        testlist=`cat matlab_log.log  | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g'  | sed 's/-//g'`
+        numtests=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
+        testlist=`cat matlab_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'`
 
         #look through numtests:
         for i in `echo $testlist`
         do
-                juLog  -test=MATLAB-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
-                juLog  -test=MATLAB-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
+                juLog -test=MATLAB-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
+                juLog -test=MATLAB-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" matlab_log.log
         done
 
         # Check that MATLAB did not exit in error
-        matlabExitedInError=`grep -E "Activation cannot proceed|license" matlab_log.log | wc -l`
+        matlabExitedInError=`grep -E "Error|Activation cannot proceed|license" matlab_log.log | wc -l`
 
         if [ $matlabExitedInError -ne 0 ]
@@ -563 +564 @@
 if [ $PYTHON_TEST -eq 1 ]; then
         #number tests:
-        numtests=`cat python_log.log  | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
-        testlist=`cat python_log.log  | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g'  | sed 's/-//g'`
+        numtests=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | wc -l`
+        testlist=`cat python_log.log | grep "\-\-\-\-\-\-\-\-starting" | sed 's/----------------starting://g' | sed 's/-//g'`
 
         #look through numtests:
         for i in `echo $testlist`
         do
-                juLog  -test=PYTHON-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
-                juLog  -test=PYTHON-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
+                juLog -test=PYTHON-$i -name=Error -error=ERROR awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
+                juLog -test=PYTHON-$i -name=Failure -error=FAILURE awk "/starting:$i/{flag=1;next}/finished/{flag=0} flag{print}" python_log.log
         done
 
         # Check that Python did not exit in error
-        pythonExitedInError=`grep -E "Traceback|bad interpreter" python_log.log | wc -l`
+        pythonExitedInError=`grep -E "Error|Traceback|bad interpreter" python_log.log | wc -l`
 
         if [ $pythonExitedInError -ne 0 ]
@@ -597 +598 @@
         $SED -i .bak 's///g' matlab_log_examples.log
 
-        numtests=`cat matlab_log_examples.log  | grep "starting: " | wc -l`
-        testlist=`cat matlab_log_examples.log   | grep "starting: " | sed 's/starting: //'`
+        numtests=`cat matlab_log_examples.log | grep "starting: " | wc -l`
+        testlist=`cat matlab_log_examples.log | grep "starting: " | sed 's/starting: //'`
 
         echo "Processing: $numtests"
         for i in `echo $testlist`
         do
-                juLog  -test=Example-$i -name=Error -error=FAILURE awk "/starting: $i/{flag=1;next}/finished: $i/{flag=0} flag{print}" matlab_log_examples.log
+                juLog -test=Example-$i -name=Error -error=FAILURE awk "/starting: $i/{flag=1;next}/finished: $i/{flag=0} flag{print}" matlab_log_examples.log
         done
 fi

issm/trunk-jpl/jenkins/macosx_pine-island

@@ -41 +41 @@
         autotools       install.sh
         cmake           install.sh
-        petsc           install-3.12-mac.sh
+        petsc           install-3.11-mac.sh
         triangle        install-mac.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux

@@ -32 +32 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-adolc-ampioff

@@ -40 +40 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         gsl                     install-linux64.sh

issm/trunk-jpl/jenkins/ross-debian_linux-adolc-ampion

@@ -41 +41 @@
         autotools               install-debian-linux.sh
         cmake                   install.sh
-        petsc                   install-3.12-linux.sh
+        petsc                   install-3.11-linux.sh
         triangle                install-linux.sh
         gsl                             install-linux64.sh

issm/trunk-jpl/jenkins/ross-debian_linux-binaries

@@ -37 +37 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux-static.sh
+        petsc           install-3.11-linux-static.sh
         triangle        install-linux-static.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-binaries-with_dakota

@@ -43 +43 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux-static.sh
+        petsc           install-3.11-linux-static.sh
         boost           install-1.55-linux-static.sh
         dakota          install-6.2-linux-static.sh

issm/trunk-jpl/jenkins/ross-debian_linux-codipack

@@ -38 +38 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-dakota

@@ -38 +38 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         boost           install-1.55-linux.sh
         dakota          install-6.2-linux.sh

issm/trunk-jpl/jenkins/ross-debian_linux-gia

@@ -33 +33 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         math77          install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-iceocean

@@ -33 +33 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-python

@@ -32 +32 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         chaco           install.sh

issm/trunk-jpl/jenkins/ross-debian_linux-solid_earth

@@ -32 +32 @@
         autotools       install-debian-linux.sh
         cmake           install.sh
-        petsc           install-3.12-linux.sh
+        petsc           install-3.11-linux.sh
         triangle        install-linux.sh
         chaco           install.sh